If you don't need the web-server turned on, simply turn it off from the config.xml
Otherwise you could rename the Server/webserver/webapps/BlueBox.war to something else (simply change the .war extension to anything else)

It would be helpful if I can shut this down as for some reason it is getting stuck on this for many minutes when I am starting the server ---

I confirm that I've seen the same behavior under certain Linux distributions. Never happened under Windows and Macosx. We are investigating.

We have exceptions into the client side (flash). When client try to connect to server and server is busy client try to connect to BlueBox but it's disabled, we want to turn off this behaviour. How can we do this?